A bit more info if you please.
What year and trim level is the jeep and how extensively is it modded? My guess would be that the ones that don't fit are factory rails?
In doing a brief search, it looks like you had to do a bit of welding for that kit. What are the reasons it is not fitting? It seems a bit odd that a kit like that would be engineered like that given the reasons for spending that kinda coin on it.